I think I just figured out why this is happening and maybe it has now turned into a LabView question. I am disabling the "measurement write to file" express VI, changing the file name, and then re-enabling it while the VI is running. When I do this, I noticed that the samples row in my file header has all zeros. If I open the file in excel and type a one (1) in each column in the samples row and then re-open the file in diadem everything works.
I would really like to be able to change the file name in my VI on the run like I have been doing and still use the original Diadem plugin to open the files later. Anyone have any ideas how to get around this?